group12_19
Chih-Hsuan Wu
Last updated: 2023-11-29
Checks: 5 2
Knit directory: DEanalysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | d7d838c | C-HW | 2023-08-11 | update graph |
| html | 7ee9782 | C-HW | 2023-07-13 | add 8_17 |
| html | 35f04ca | C-HW | 2023-07-12 | add 12_19 |
Data summary
Mean difference in raw data/normalized data
Number of hits from each method
Histogram of p-value/adj.p-value
Violin plot of log2mean of DEGs
Violin plot of gene expression frequency of DEGs
Heatmap of top hits
Poisson-glmm DEGs
Additional DEGs from other methods
Binomial-glmm
DEGs in pois_glmm exclusive to MMpoisson
In the MMpoisson model, cell type is considered as a random effect. This approach treats certain aspects of cell type variations as random factors. Consequently, it may obscure the true variation in cell types, limiting its ability to accurately reveal the specific differences between different cell types.
Additionally, the library size is employed as an offset to normalize the counts. That is, the model is considering rate instead of counts. Suppose some genes are highly expressed in one cell type than the other, the absolute difference could be eliminate after accounting for library size. This normalization approach may inadvertently mask certain gene expression differences between cell types.
| Version | Author | Date |
|---|---|---|
| d7d838c | C-HW | 2023-08-11 |
Enrichment analysis
enrichKEGG object
| Version | Author | Date |
|---|---|---|
| d7d838c | C-HW | 2023-08-11 |
| Version | Author | Date |
|---|---|---|
| d7d838c | C-HW | 2023-08-11 |
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] pathview_1.38.0 org.Hs.eg.db_3.16.0
[3] AnnotationDbi_1.60.2 enrichplot_1.18.4
[5] clusterProfiler_4.6.2 reshape_0.8.9
[7] gridExtra_2.3 pheatmap_1.0.12
[9] SingleCellExperiment_1.20.1 SummarizedExperiment_1.28.0
[11] Biobase_2.58.0 GenomicRanges_1.50.2
[13] GenomeInfoDb_1.34.9 IRanges_2.32.0
[15] S4Vectors_0.36.2 BiocGenerics_0.44.0
[17] MatrixGenerics_1.10.0 matrixStats_1.0.0
[19] ggpubr_0.6.0 dplyr_1.1.2
[21] ggplot2_3.4.2
loaded via a namespace (and not attached):
[1] shadowtext_0.1.2 backports_1.4.1 fastmatch_1.1-3
[4] workflowr_1.7.0 plyr_1.8.8 igraph_1.5.0
[7] lazyeval_0.2.2 splines_4.2.2 BiocParallel_1.32.6
[10] digest_0.6.33 yulab.utils_0.0.6 htmltools_0.5.5
[13] GOSemSim_2.24.0 viridis_0.6.3 GO.db_3.16.0
[16] fansi_1.0.4 magrittr_2.0.3 memoise_2.0.1
[19] Biostrings_2.66.0 graphlayouts_1.0.0 colorspace_2.1-0
[22] blob_1.2.4 ggrepel_0.9.3 xfun_0.39
[25] crayon_1.5.2 RCurl_1.98-1.12 jsonlite_1.8.7
[28] graph_1.76.0 scatterpie_0.2.1 ape_5.7-1
[31] glue_1.6.2 polyclip_1.10-4 gtable_0.3.3
[34] zlibbioc_1.44.0 XVector_0.38.0 DelayedArray_0.24.0
[37] car_3.1-2 Rgraphviz_2.42.0 abind_1.4-5
[40] scales_1.2.1 DOSE_3.24.2 DBI_1.1.3
[43] rstatix_0.7.2 Rcpp_1.0.11 viridisLite_0.4.2
[46] gridGraphics_0.5-1 tidytree_0.4.4 bit_4.0.5
[49] httr_1.4.6 fgsea_1.24.0 RColorBrewer_1.1-3
[52] XML_3.99-0.14 pkgconfig_2.0.3 farver_2.1.1
[55] sass_0.4.7 utf8_1.2.3 labeling_0.4.2
[58] ggplotify_0.1.1 tidyselect_1.2.0 rlang_1.1.1
[61] reshape2_1.4.4 later_1.3.1 munsell_0.5.0
[64] tools_4.2.2 cachem_1.0.8 downloader_0.4
[67] cli_3.6.1 generics_0.1.3 RSQLite_2.3.1
[70] gson_0.1.0 broom_1.0.5 evaluate_0.21
[73] stringr_1.5.0 fastmap_1.1.1 yaml_2.3.7
[76] ggtree_3.6.2 knitr_1.27 bit64_4.0.5
[79] fs_1.6.3 tidygraph_1.2.3 purrr_1.0.1
[82] KEGGREST_1.38.0 ggraph_2.1.0 nlme_3.1-162
[85] whisker_0.4.1 KEGGgraph_1.58.3 aplot_0.1.10
[88] compiler_4.2.2 rstudioapi_0.15.0 png_0.1-8
[91] ggsignif_0.6.4 treeio_1.22.0 tibble_3.2.1
[94] tweenr_2.0.2 bslib_0.5.0 stringi_1.7.12
[97] highr_0.10 lattice_0.21-8 Matrix_1.5-4.1
[100] vctrs_0.6.3 pillar_1.9.0 lifecycle_1.0.3
[103] jquerylib_0.1.4 data.table_1.14.8 cowplot_1.1.1
[106] bitops_1.0-7 httpuv_1.6.11 patchwork_1.1.2
[109] qvalue_2.30.0 R6_2.5.1 promises_1.2.0.1
[112] codetools_0.2-19 MASS_7.3-60 rprojroot_2.0.3
[115] withr_2.5.0 GenomeInfoDbData_1.2.9 parallel_4.2.2
[118] grid_4.2.2 ggfun_0.1.1 tidyr_1.3.0
[121] HDO.db_0.99.1 rmarkdown_2.23 carData_3.0-5
[124] ggnewscale_0.4.9 git2r_0.32.0 ggforce_0.4.1